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pfuriopfurio
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Merge branch 'develop' into TASK-7645
2 parents 5816368 + a429a6e commit f6b9081

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‎.github/workflows/debug-token.yml‎

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name: Debug ZETTA_REPO_ACCESS_TOKEN and Permissions
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on:
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workflow_dispatch:
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jobs:
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debug-token-and-permissions:
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runs-on: ${{ vars.UBUNTU_VERSION }}
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env:
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ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 1
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- name: Show runner and workflow context
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run: |
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echo "Runner: $(uname -a)"
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echo "GitHub Actor: $GITHUB_ACTOR"
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echo "Workflow: $GITHUB_WORKFLOW"
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echo "Event: $GITHUB_EVENT_NAME"
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echo "Repository: $GITHUB_REPOSITORY"
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echo "Job: $GITHUB_JOB"
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echo "Workspace: $GITHUB_WORKSPACE"
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echo "Home: $HOME"
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echo "Shell: $SHELL"
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echo "GitHub Ref: $GITHUB_REF"
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echo "GitHub SHA: $GITHUB_SHA"
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echo "GitHub Run ID: $GITHUB_RUN_ID"
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echo "GitHub Run Number: $GITHUB_RUN_NUMBER"
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- name: Show GitHub Actions permissions
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run: |
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echo "Permissions JSON:"
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cat $GITHUB_EVENT_PATH | jq '.workflow_run?.permissions // .permissions // "No permissions found"'
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- name: Check ZETTA_REPO_ACCESS_TOKEN presence and length
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run: |
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if [ -z "$ZETTA_REPO_ACCESS_TOKEN" ]; then
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echo "ZETTA_REPO_ACCESS_TOKEN is NOT set"
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exit 1
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else
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echo "ZETTA_REPO_ACCESS_TOKEN is set"
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echo "Length: ${#ZETTA_REPO_ACCESS_TOKEN}"
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echo "First 4 chars: ${ZETTA_REPO_ACCESS_TOKEN:0:4}"
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fi
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- id: get_ci_core_xetabase_branch
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name: "Get CI-CORE current branch for Xetabase from target branch"
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run: |
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chmod +x ./.github/workflows/scripts/get_opencga_enterprise_branch.sh
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echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}"
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xetabase_branch=$(./.github/workflows/scripts/get_opencga_enterprise_branch.sh "java-common-libs" "develop" "TASK-8067")
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echo "__CI CORE Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
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REPO_URI="https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git"
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echo "$(git ls-remote "$REPO_URI" "TASK-8067")"
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env:
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ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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- id: get_xetabase_branch
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name: "Get JCL current branch for Xetabase from target branch"
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run: |
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chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
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echo "github.event.pull_request.base.ref: develop"
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echo "github.event.pull_request.head.ref: TASK-8067"
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echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}"
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xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "develop" "TASK-8067")
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echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
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env:
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ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
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- name: Clone OpenCGA Enterprise branch '${{ inputs.branch }}'
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uses: actions/checkout@v4
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with:
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repository: zetta-genomics/opencga-enterprise
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ref: TASK-8067
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token: ${{ env.ZETTA_REPO_ACCESS_TOKEN }}
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path: xetbase-opencga-enterprise
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fetch-depth: "10"
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- name: Try to clone the private repo with token
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run: |
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set -x
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git clone https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git || true
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- name: Show authenticated user (if possible)
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run: |
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curl -H "Authorization: token $ZETTA_REPO_ACCESS_TOKEN" https://api.github.com/user
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- name: Show environment variables (filtered)
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run: |
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env | grep -E 'GITHUB|ZETTA|RUNNER|CI'

‎.github/workflows/scripts/get_opencga_enterprise_branch.sh‎

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#!/usr/bin/env bash
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# get_opencga_enterprise_branch.sh
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#
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# This script computes the correct opencga-enterprise branch to use for testing a PR in any Xetabase component repo.
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# It unifies the logic previously duplicated in java-common-libs, biodata, and opencga.
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#
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# Inputs:
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# 1. project (artifactId from pom.xml)
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# 2. base_ref (target branch of the PR)
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# 3. head_ref (source branch of the PR)
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#
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# Output:
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# Prints the resolved opencga-enterprise branch to stdout.
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# Exits with non-zero and error message if it cannot resolve a branch.
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set -euo pipefail
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project="$1"
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base_ref="$2"
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head_ref="$3"
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REPO_URI="https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git"
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# 1. If the branch begins with 'TASK' and exists in the opencga-enterprise repository, return it
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if [[ $head_ref == TASK* ]]; then
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if [ "$(git ls-remote "$REPO_URI" "$head_ref")" ] ; then
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echo "$head_ref";
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exit 0
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fi
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fi
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# 2. If the base_ref is 'develop', always map to develop
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if [[ "$base_ref" == "develop" ]]; then
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echo "develop"
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exit 0
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fi
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# 3. release-* branch logic
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if [[ "$base_ref" =~ ^release-([0-9]+)\. ]]; then
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major="${BASH_REMATCH[1]}"
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# Project-specific offset for release branch mapping
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case "$project" in
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java-common-libs)
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offset=3
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;;
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biodata|opencga)
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offset=1
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;;
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opencga-enterprise)
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# If the project is opencga-enterprise, use the branch as-is
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echo "$base_ref"
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exit 0
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;;
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*)
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echo "ERROR: Unknown project '$project' for release branch mapping" >&2
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exit 1
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;;
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esac
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new_major=$((major - offset))
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if (( new_major < 1 )); then
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echo "ERROR: Computed release branch version < 1 for $project (base_ref: $base_ref, offset: $offset)" >&2
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exit 1
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fi
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# Extract the rest of the version (minor and patch) from base_ref
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rest_version=$(echo "$base_ref" | sed -E "s/^release-[0-9]+(\..*)/\1/")
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target_branch="release-${new_major}${rest_version}"
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# Check if the exact branch exists (fix: do not escape quotes)
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if [ "$(git ls-remote --heads "$REPO_URI" "$target_branch")" ]; then
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echo "$target_branch"
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exit 0
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else
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echo "ERROR: No matching release branch '$target_branch' found in opencga-enterprise for $project (base_ref: $base_ref, offset: $offset)" >&2
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exit 1
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fi
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fi
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# 4. Fallback: fail with clear error
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echo "ERROR: Could not resolve opencga-enterprise branch for project '$project' (base_ref: $base_ref, head_ref: $head_ref)" >&2
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exit 1
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